Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Nypa fruticans(Wurmb),a mangrove palm species with origins dating back to the Late Cretaceous period,is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms.Here,we present a chromosome-level genome sequence and assembly for N.fruticans.We integrated the genomes of N.fruticans and other palm family members for a comparative genomic analysis,which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago,shaping the distinctive characteristics observed in this clade.We also inferred a low mutation rate for the N.fruticans genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary period.Moreover,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in N.fruticans.Furthermore,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in N.fruticans underly its crypto-vivipary characteristics,reflecting its intertidal adaptation.Our study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove palm.Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

Efficacy of acupuncture in refractory irritable bowel syndrome patients:a randomized controlled trial

Previous studies have confirmed that acupuncture for irritable bowel syndrome(IBS)provided an additional benefit over usual care alone.Therefore,we performed a multicenter,randomized,sham-controlled trial to assess the efficacy and safety of acupuncture versus sham acupuncture for refractory IBS in patients in the context of conventional treatments.Patients in the acupuncture and sham acupuncture groups received real or sham acupuncture treatment in 3 sessions per week for a total of 12 sessions.The primary outcome was a change in the IBS–Symptom Severity Scale(IBS-SSS)score from baseline to week 4.A total of 521 participants were screened,and 170 patients(85 patients per group)were enrolled and included in the intention-to-treat analysis.Baseline characteristics were comparable across the two groups.From baseline to 4 weeks,the IBS-SSS total score decreased by 140.0(95%CI:126.0 to 153.9)in the acupuncture group and 64.4(95%CI:50.4 to 78.3)in the sham acupuncture group.The between-group difference was 75.6(95%CI:55.8 to 95.4).Acupuncture efficacy was maintained during the 4-week follow-up period.There were no serious adverse events.In conclusion,acupuncture provided benefits when combined with treatment as usual,providing more options for the treatment of refractory IBS.

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and persistence.Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification,phenotypic convergence,and inter-species interaction.As the genome sequences of more and more non-model organisms are becoming available,the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning.In this study,we reviewed the latest research advances in wild animals and plants,focusing on adaptive traits,convergent evolution,and coevolution.Firstly,we focused on the adaptive evolution of morphological,behavioral,and physiological traits.Secondly,we reviewed the phenotypic convergences of life history traits and responding to environmental pressures,and the underlying molecular convergence mechanisms.Thirdly,we summarized the advances of coevolution,including the four main types:mutualism,parasitism,predation and competition.Overall,these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction,demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies.Finally,we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees

Mangroves are adapted to intertidal zones,which present extreme environmental conditions.WRKYs are among the most prominent transcription factors(TFs)in higher plants and act through various interconnected networks to regulate responses to multiple abiotic stressors.Here,based on omic data,we investigated the landscape and evolutionary patterns of WRKYs in the main mangrove genus Avicennia.We found that both the number and the proportion of TFs and WRKYs in Avicennia species exceeded their inland relatives,indicating a signifcant expansion of WRKYs in Avicennia.We identifed 109 WRKY genes in the representative species Avicennia marina.Comparative genomic analysis showed that two recent wholegenome duplication(WGD)events played a critical role in the expansion of WRKYs,and 88%of Avicennia marina WRKYs(AmWRKYs)have been retained following these WGDs.Applying comparative transcriptomics on roots under experimental salt gradients,we inferred that there is high divergence in the expression of WGD-retained AmWRKYs.Moreover,we found that the expression of 16 AmWRKYs was stable between freshwater and moderately saline water but increased when the trees were exposed to high salinity.In particular,14 duplicates were retained following the two recent WGD events,indicating potential neo-and sub-functionalization.We also found that WRKYs could interact with other upregulated genes involved in signalling pathways and natural antioxidant biosynthesis to enhance salt tolerance,contributing to the adaptation to intertidal zones.Our omic data of the WRKY family in A.marina broadens the understanding of how a TF family relates to the adaptive evolution of mangroves.

Assembly processes underlying bacterial community differentiation among geographically close mangrove forests

Bacterial communities play pivotal roles in nutrient cycling in mangrove forests.The assembly of mangrove microbial communities has been found to be influenced by complex factors,such as geographic distance,physicochemical conditions,and plant identity,but the relative importance of these factors and how these factors shape the assembling process remain elusive.We analyzed the bacterial communities sampled from three mangrove species(Aegiceras corniculatum,Bruguiera sexangula,and Kandelia obovata)at three locations along the estuarine Dongzhai Harbor in Hainan,China.We revealed larger differences in rhizosphere bacterial communities among geographical locations than among plant species,indicated by differences in diversity,composition,and interaction networks.We found that dispersal limitation and homogeneous selection have substantial contributions to the assembly of mangrove rhizosphere bacterial communities in all three locations.Following the phylogenetic‐bin‐based null model analysis(iCAMP)framework,we also found dispersal limitation and homogeneous selection showing dominance in some bins.The greater differences among geographic locations may be mainly attributed to the larger proportions of dispersal limitation even at such a short geographic distance.We also found that beta diversity was positively correlated with environmental distances,implying that the more similar environmental conditions(such as rich carbon and nitrogen contents)among plant species may have shaped similar bacterial communities.We concluded that the geographic distances,which are associated with dispersal limitation,played a key role in assembling mangrove rhizosphere bacterial communities,while physicochemical conditions and plant identity contributed less.

Genomic Convergence in the Adaptation to Extreme Environments

Convergent evolution is especially common in plants that have independently adapted to the same extreme environments(i.e.,extremophile plants).The recent burst of omics data has alleviated many limitations that have hampered molecular convergence studies of non-model extremophile plants.In this review,we summarize cases of genomic convergence in these taxa to examine the extent and type of genomic convergence during the process of adaptation to extreme environments.Despite being well studied by candidate gene approaches,convergent evolution at individual sites is rare and often has a high false-positive rate when assessed in whole genomes.By contrast,genomic convergence at higher genetic levels has been detected during adaptation to the same extreme environments.Examples include the convergence of biological pathways and changes in gene expression,gene copy number,amino acid usage,and GC content.Higher convergence levels play important roles in the adaptive evolution of extremophiles and may be more frequent and involve more genes.In several cases,multiple types of convergence events have been found to co-occur.However,empirical and theoretical studies of this higher level convergent evolution are still limited.In conclusion,both the development of powerful approaches and the detection of convergence at various genetic levels are needed to further reveal the genetic mechanisms of plant adaptation to extreme environments.